Clavius Base is located in the Clavius crater, due south of Tycho. According to the novel, the base was finished in 1994 by the United States Astronautical Engineering Corps. If necessary, the base can be self-sustaining. In the film, the base features some surface features, such as a landing pad, control tower, and ancillary support structures, but the vast majority of the base is located beneath the Lunar surface to protect it from micro-meteoroid impacts and solar radiation. Incoming spacecraft set down on a landing platform beneath a dome which opens as the vessel descends. The landing platform is part of an enormous elevator, which lowers the spacecraft into a cavernous docking bay.

When the Tycho Monolith (TMA-1) was discovered in 2001, all outside contact with Clavius was shut down. Whenever someone tried to contact the base, all one could get was a recording that said the phone lines were "temporarily out of order". A cover story was placed that an epidemic had broken out at the Base.

Dr. Heywood Floyd traveled to the Clavius Base to investigate the monolith about 18 months prior to the Discovery mission in 2001. While present at the base, Floyd met with American lunar officials and notified them that the government was requiring individual security oaths to be taken from each individual on the base. After the breifing, Floyd was transported to the Tycho crater on a moonbus.